Phase-amplitude coupling

This tutorial introduces the concept of phase-amplitude coupling (PAC) and the metrics used in Brainstorm to estimate it. Those tools are illustrated on three types of data: simulated recordings, rat intra-cranial recordings and MEG signals.

Phase-amplitude coupling

Illustrated introduction and mathematical background.

Simulated recordings

Step-by-step instructions with as many screen captures as possible: generation and analysis of the signals.

Rat recordings

How to download the data.

Step-by-step instructions to analyze the recordings.

MEG recordings (NOTE - BEING UPDATED)

Step-by-step instructions to analyze the wMNE source signals for Phase Amplitude Coupling.

In order to do this part of the tutorial you will need to get the file sample_resting.zip from the Download page.

Preparation of the anatomy, basic pre-processing and source modeling will be only mentioned briefly and will be similar to the continuous recordings tutorials found here: Continuous Recordings Tutorial

Step 1: Pre-processing

The first steps of include importing the anatomy and the functional data and projecting the sources. If you unsure how to do this the detailed steps can be found in the Continuous Recordings tutorial or within the tutorials for the '12 Easy steps for Brainstorm', all of which are available from this page: Tutorials

Anatomy

• Import the freesurfer anatomy folder and define the fiducial points.
• The MRI coordinates be (+/- a few millimeters):
  • NAS: x=128, y=225, z=135
  • LPA: x=54, y=115, z=107
  • RPA: x=204, y=115, z=99
  • AC: x=133, y=137, z=152
  • PC: x=132, y=108, z=150
  • IH: x=133, y=163, z=196 (anywhere on the midsagittal plane)

Functional data

• The sample_resting download contains two 10 minute resting state runs. We are going to use the first one which is the one labelled 'subj002_spontaneous_20111102_02_AUX.ds'.
• Use the review raw file to access this file through the brainstorm interface. Click yes to refine registration with the head points.

Pre-Processing

• All data should be checked for artifacts and examined for quality prior to doing analyses such as PAC (including marking bad segments, and correcting for artifacts such as eye blinks and heartbeats with SSPs.
• In the channel file for this data set the ECG channel is called 'EEG057' and the VEOG channel is called 'EEG058'.
• Use the detect eye blinks and detect heartbeat functions from the SSP option in the event tab with these channel names to detect the heartbeats and eye blinks.
• Then use the ‘Compute SSP: Eyeblinks’ and ‘Compute SSP: Heartbeats’ to project away these artifacts from the data. Make sure to write 'MEG' in the 'Sensor Types or Names' option box if it is not already. For consistency with this tutorial use (only) the first component for each.

• For more information / guidance regarding artifacts and SSPs, view this tutorial: Artifact Tutorial

Project Sources

Step 2: Using the PAC Function

Once you have the sources projected onto the anatomy proceed with the following instructions to use the PAC function on the source data.

The Function

• The function for Phase Amplitude Coupling analysis is found in the frequency menu in the process selection menu.

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• Drag and drop the sources file into the dropbox in the process 1 tab. Click on run, go to frequency and click on Phase Amplitude Coupling. You should get the following option box appear.

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Process Options

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• Time Window: The time segment of the input file to be analyzed for PAC

  Nesting Frequency Band (low): The frequency band of interest for the frequency for phase (the low, nesting frequencies).

  • This can be a wide exploratory range (for example 2 - 30 Hz) or a much smaller and specific range (for example, theta, 4-8Hz)

  Nested Frequency Band (high): The frequency band of interest for the frequencies for amplitude (the high, nested frequencies).

  • The frequency band of interest for the frequencies for amplitude (the high, nested frequencies). This can be a wide exploratory range (for example, 40 - 250 Hz) or a smaller and specifc range (for example, low gamma, 40-80Hz)

  • Note: The nested frequency can only be as high as your sampling rate has the resolution to yield.

  Processing Options

  • Parallel processing toolbox

    Use Mex files

    Number of signals to process at once

  Output Options

  • Save average PAC across trials

    Save the full PAC maps

Step 3: Verifying with Canolty Maps

The Function

Description of the Options